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lammps/examples/kim/log.10Feb21.in.kim-sm.melt.clang.4
Yaser Afshar c16064d493 update kim examples log files
2021-02-25 08:23:26 -06:00

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LAMMPS (10 Feb 2021)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Simulator Model (PM)
# `Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000`
# is installed. This can be done with the command
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# See `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
#=== BEGIN kim init ==========================================
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# For Simulator : LAMMPS 28 Feb 2019
# Running on : LAMMPS 10 Feb 2021
#
units real
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
atom_style charge
neigh_modify one 4000
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
kim interactions O
#=== BEGIN kim interactions ==================================
variable kim_periodic equal 1
pair_style reax/c /var/tmp/kim-shared-library-parameter-file-directory-hIWMxB258NXk/lmp_control safezone 2.0 mincap 100
pair_coeff * * /var/tmp/kim-shared-library-parameter-file-directory-hIWMxB258NXk/ffield.reax.rdx O
Reading potential file /var/tmp/kim-shared-library-parameter-file-directory-hIWMxB258NXk/ffield.reax.rdx with DATE: 2010-02-19
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /var/tmp/kim-shared-library-parameter-file-directory-hIWMxB258NXk/param.qeq
#=== END kim interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/SM_107643900657_000#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Simulator Model originally published in \cite{SM_107643900657_000a} is archived in OpenKIM~\cite{SM_107643900657_000, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-SM_107643900657_000.bib}
\end{document}
}
@Misc{SM_107643900657_000,
author = {Ellad Tadmor},
title = {{LAMMPS} {R}eax{FF} potential for {RDX} ({C}-{H}-{N}-{O}) systems developed by {S}trachan et al. (2003) v000},
doi = {10.25950/acd3fc89},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/acd3fc89}},
keywords = {OpenKIM, Simulator Model, SM_107643900657_000},
publisher = {OpenKIM},
year = 2019,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{SM_107643900657_000a,
author = {Strachan, Alejandro and van Duin, Adri C. T. and Chakraborty, Debashis and Dasgupta, Siddharth and Goddard, William A.},
doi = {10.1103/PhysRevLett.91.098301},
issue = {9},
journal = {Physical Review Letters},
month = {Aug},
numpages = {4},
pages = {098301},
publisher = {American Physical Society},
title = {Shock Waves in High-Energy Materials: {T}he Initial Chemical Events in Nitramine {RDX}},
volume = {91},
year = {2003},
}
- pair reax/c command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reax command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 4000, page size: 100000
master list distance cutoff = 10.3
ghost atom cutoff = 10.3
binsize = 5.15, bins = 18 18 18
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 630.2 | 630.2 | 630.2 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -39091.147 0 -20014.559 19501.107
100 63.198252 -26042.062 0 -20014.027 21497.661
Loop time of 14.1676 on 4 procs for 100 steps with 32000 atoms
Performance: 0.610 ns/day, 39.355 hours/ns, 7.058 timesteps/s
99.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.3935 | 9.3935 | 9.3936 | 0.0 | 66.30
Neigh | 0.15786 | 0.15879 | 0.16003 | 0.2 | 1.12
Comm | 0.025777 | 0.025906 | 0.025992 | 0.1 | 0.18
Output | 2.8e-05 | 3.35e-05 | 4.6e-05 | 0.0 | 0.00
Modify | 4.5801 | 4.5814 | 4.5823 | 0.0 | 32.34
Other | | 0.00801 | | | 0.06
Nlocal: 8000.00 ave 8010 max 7993 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 12605.0 ave 12612 max 12595 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 1.00097e+06 ave 1.00187e+06 max 1.0006e+06 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 4003876
Ave neighs/atom = 125.12113
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:14
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